Plot UMAP

Download UMAP.

scp schea2@hpc3.rcic.uci.edu:/share/crsp/lab/alcalof/schea2/20220414-seurat/umap-by-embryo-all-aggr.Robj .

Load libraries.

library(tidyverse)

Registered S3 methods overwritten by 'dbplyr':
  method         from
  print.tbl_lazy     
  print.tbl_sql      
── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.6     ✔ purrr   0.3.4
✔ tibble  3.1.7     ✔ dplyr   1.0.9
✔ tidyr   1.2.0     ✔ stringr 1.4.0
✔ readr   2.1.1     ✔ forcats 0.5.1
── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Warning message:
R graphics engine version 14 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed. 

library(scales)

Attaching package: ‘scales’

The following object is masked from ‘package:purrr’:

    discard

The following object is masked from ‘package:readr’:

    col_factor

Load UMAP.

load("/Volumes/all_ssd/20220414-seurat/umap-by-embryo-all-aggr.Robj")

Plot UMAP by stage.

stage.umap <- ggplot() +
  geom_point(data = sample(whole.umap), mapping = aes(x = umap.1, y = umap.2, color = stage), shape = 20, stroke = 0, size = 0.5) +
  labs(x = "UMAP 1", y = "UMAP 2", color = "Stage") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"))
stage.umap
ggsave(plot = stage.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-by-stage-all-aggr.png", device = "png", width = 3.25, height = 2.25)

Plot UMAP by genotype.

stage.umap <- ggplot() +
  geom_point(data = whole.umap, mapping = aes(x = umap.1, y = umap.2, color = stage), shape = 20, stroke = 0, size = 0.5) +
  facet_wrap(~stage, nrow = 1) +
  labs(x = "UMAP 1", y = "UMAP 2", color = "Genotype") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"), strip.background = element_blank())
stage.umap
ggsave(plot = stage.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-facet-stage-all-aggr.png", device = "png", width = 6.5, height = 2.25)

Plot UMAP by genotype.

genotype.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "LB")), mapping = aes(x = umap.1, y = umap.2, color = genotype), shape = 20, stroke = 0, size = 0.5) +
  scale_color_manual(values = c("royalblue", "indianred")) +
  labs(title = "Late Bud", x = "UMAP 1", y = "UMAP 2", color = "Genotype") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"))
genotype.umap
ggsave(plot = genotype.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-by-genotype-late-bud-all-aggr.png", device = "png", width = 3.25, height = 2.25)

Plot UMAP by genotype.

genotype.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "LB")), mapping = aes(x = umap.1, y = umap.2, color = genotype), shape = 20, stroke = 0, size = 0.5) +
  facet_wrap(~genotype, nrow = 1) +
  scale_color_manual(values = c("royalblue", "indianred")) +
  labs(title = "Late Bud", x = "UMAP 1", y = "UMAP 2", color = "Genotype") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"), strip.background = element_blank())
genotype.umap
ggsave(plot = genotype.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-facet-genotype-late-bud-all-aggr.png", device = "png", width = 6.5, height = 2.25)

Plot UMAP by embryo.

embryo.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "LB") %>% filter(genotype == "Nipbl Flox/+")), mapping = aes(x = umap.1, y = umap.2, color = embryo), shape = 20, stroke = 0, size = 0.5) +
  scale_color_manual(values = hue_pal()(28)[c(1, 15, 3, 17, 5)]) +
  labs(title = "Nipbl Flox/+, Late Bud", x = "UMAP 1", y = "UMAP 2", color = "Embryo") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"))
embryo.umap
ggsave(plot = embryo.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-by-embryo-flox-late-bud-all-aggr.png", device = "png", width = 3.25, height = 2.25)

Plot UMAP by embryo.

embryo.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "LB") %>% filter(genotype == "Nipbl Flox/+")), mapping = aes(x = umap.1, y = umap.2, color = embryo), shape = 20, stroke = 0, size = 0.5) +
  facet_wrap(~embryo, ncol = 4) +
  scale_color_manual(values = hue_pal()(28)[c(1, 15, 3, 17, 5)]) +
  labs(title = "Nipbl Flox/+, Late Bud", x = "UMAP 1", y = "UMAP 2", color = "Embryo") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"), strip.background = element_blank())
embryo.umap
ggsave(plot = embryo.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-facet-embryo-flox-late-bud-all-aggr.png", device = "png", width = 6.5, height = 3.6)

Plot UMAP by embryo.

embryo.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "LB") %>% filter(genotype == "Nipbl FIN/+")), mapping = aes(x = umap.1, y = umap.2, color = embryo), shape = 20, stroke = 0, size = 0.5) +
  scale_color_manual(values = hue_pal()(28)[c(19, 7, 21, 9, 23, 11)]) +
  labs(title = "Nipbl FIN/+, Late Bud", x = "UMAP 1", y = "UMAP 2", color = "Embryo") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"))
embryo.umap
ggsave(plot = embryo.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-by-embryo-fin-late-bud-all-aggr.png", device = "png", width = 3.25, height = 2.25)

Plot UMAP by embryo.

embryo.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "LB") %>% filter(genotype == "Nipbl FIN/+")), mapping = aes(x = umap.1, y = umap.2, color = embryo), shape = 20, stroke = 0, size = 0.5) +
  facet_wrap(~embryo, ncol = 4) +
  scale_color_manual(values = hue_pal()(28)[c(19, 7, 21, 9, 23, 11)]) +
  labs(title = "Nipbl FIN/+, Late Bud", x = "UMAP 1", y = "UMAP 2", color = "Embryo") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"), strip.background = element_blank())
embryo.umap
ggsave(plot = embryo.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-facet-embryo-fin-late-bud-all-aggr.png", device = "png", width = 6.5, height = 3.6)

Plot UMAP by genotype.

genotype.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "CC")), mapping = aes(x = umap.1, y = umap.2, color = genotype), shape = 20, stroke = 0, size = 0.5) +
  scale_color_manual(values = c("royalblue", "indianred")) +
  labs(title = "Cardiac Crescent", x = "UMAP 1", y = "UMAP 2", color = "Genotype") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"))
genotype.umap
ggsave(plot = genotype.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-by-genotype-cardiac-crescent-all-aggr.png", device = "png", width = 3.25, height = 2.25)

Plot UMAP by genotype.

genotype.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "CC")), mapping = aes(x = umap.1, y = umap.2, color = genotype), shape = 20, stroke = 0, size = 0.5) +
  facet_wrap(~genotype, ncol = 2) +
  scale_color_manual(values = c("royalblue", "indianred")) +
  labs(title = "Cardiac Crescent", x = "UMAP 1", y = "UMAP 2", color = "Genotype") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"), strip.background = element_blank())
genotype.umap
ggsave(plot = genotype.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-facet-genotype-cardiac-crescent-all-aggr.png", device = "png", width = 6.5, height = 2.25)

Plot UMAP by embryo.

embryo.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "CC") %>% filter(genotype == "Nipbl Flox/+")), mapping = aes(x = umap.1, y = umap.2, color = embryo), shape = 20, stroke = 0, size = 0.5) +
  scale_color_manual(values = hue_pal()(28)[c(25, 13, 27, 2, 16, 4, 18, 6)]) +
  labs(title = "Nipbl Flox/+, Cardiac Crescent", x = "UMAP 1", y = "UMAP 2", color = "Embryo") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"))
embryo.umap
ggsave(plot = embryo.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-by-embryo-flox-cardiac-crescent-all-aggr.png", device = "png", width = 3.25, height = 2.25)

Plot UMAP by embryo.

embryo.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "CC") %>% filter(genotype == "Nipbl Flox/+")), mapping = aes(x = umap.1, y = umap.2, color = embryo), shape = 20, stroke = 0, size = 0.5) +
  facet_wrap(~embryo, ncol = 4) +
  scale_color_manual(values = hue_pal()(28)[c(25, 13, 27, 2, 16, 4, 18, 6)]) +
  labs(title = "Nipbl Flox/+, Cardiac Crescent", x = "UMAP 1", y = "UMAP 2", color = "Embryo") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"), strip.background = element_blank())
embryo.umap
ggsave(plot = embryo.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-facet-embryo-flox-cardiac-crescent-all-aggr.png", device = "png", width = 6.5, height = 3.6)

Plot UMAP by embryo.

embryo.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "CC") %>% filter(genotype == "Nipbl FIN/+")), mapping = aes(x = umap.1, y = umap.2, color = embryo), shape = 20, stroke = 0, size = 0.5) +
  scale_color_manual(values = hue_pal()(28)[c(20, 8, 22, 10, 24, 12, 26, 14)]) +
  labs(title = "Nipbl FIN/+, Cardiac Crescent", x = "UMAP 1", y = "UMAP 2", color = "Embryo") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"))
embryo.umap
ggsave(plot = embryo.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-by-embryo-fin-cardiac-crescent-all-aggr.png", device = "png", width = 3.25, height = 2.25)

Plot UMAP by embryo.

embryo.umap <- ggplot() +
  geom_point(data = sample(whole.umap %>% filter(stage == "CC") %>% filter(genotype == "Nipbl FIN/+")), mapping = aes(x = umap.1, y = umap.2, color = embryo), shape = 20, stroke = 0, size = 0.5) +
  facet_wrap(~embryo, ncol = 4) +
  scale_color_manual(values = hue_pal()(28)[c(20, 8, 22, 10, 24, 12, 26, 14)]) +
  labs(title = "Nipbl FIN/+, Cardiac Crescent", x = "UMAP 1", y = "UMAP 2", color = "Embryo") +
  guides(color = guide_legend(override.aes = list(size=2.3))) +
  theme_classic(base_size = 7) +
  theme(axis.line = element_blank(), axis.ticks = element_blank(), axis.text = element_blank(), plot.title = element_text(hjust = 0.5), legend.key.size = unit(7, "pt"), strip.background = element_blank())
embryo.umap
ggsave(plot = embryo.umap, filename = "/Volumes/all_ssd/20220414-seurat/umap-facet-embryo-fin-cardiac-crescent-all-aggr.png", device = "png", width = 6.5, height = 3.6)